The variants detected fro ctDNA are at very low fractions. So my question is: Can anyone share some insight on how to distinguish between variants at very low fractions and noise (perhaps sequencing error)? It will be really helpful if one or two software are recommended specifically for detecting these variant and the way these software works. Many thanks :)
The main software we use for detecting low frequency variants is LoFreq: http://csb5.github.io/lofreq/
LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.
Other ones you could check out are FreeBayes: https://github.com/ekg/freebayes and VarScan: http://varscan.sourceforge.net
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FreeBayes and VarScan are for detecting somatic mutation from tumor sample indeed. I am wondering if there is any variant caller that is specifically designed to detect variant from ctDNA (very low variant allele fraction)
I don't know of any specific to ctDNA - but why would you think you need a specialised one for that - aside from the low frequency aspect, what is different about a ctDNA sample? We have used FreeBayes, LoFreq and VarScan on population samples to detect variants down to 1% frequency in the population (below that we get quite very worried about noise).